jvarkit
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lindenb
Java utilities for Bioinformatics
### Verify * if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue * the version of java ### Subject of the issue Executing minicaller after obtaining the...
### Verify * if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue * the version of java ### Subject of the issue specify list of scaffolds for...
Hello, I have a problem when installing a tool, when I run the code ./gradlew msa2vcf I get this error? Downloading https://services.gradle.org/distributions/gradle-6.7-bin.zip Exception in thread "main" java.net.ConnectException: Connection timed out...
Hello. I found your bioalcidaejdk.jar very useful to make a table that summarizes the numbers of homozygous and heterozygous non-reference from a multi-sample VCF file. I used the following code...
### Subject of the issue found non-ASCII code after verticalGridLinesVisible in XYPlot.java ### Your environment * version of jvarkit * version of java: openjdk-11.0.8_10 * the value of `${JAVA_HOME}`: /opt/spack/opt/spack/linux-centos7-broadwell/intel-19.0.5/openjdk-11.0.8_10-bwcgovtzmcjykzhldbpotpcscyvo6yko...
### set seed for biostar145820.jar I am using biostar145820.jar to subsample bam files, and it works great. I was just wondering if there is a seed in the random shuffle...
### Subject of the issue I have some peptides from a proteomics experiment (~5000) and I have a list of protein references that they may align to, sometimes not perfectly....
``` javac -version javac 11.0.2 java -version openjdk version "1.8.0_191" ``` so you compiled with a modern java compiler (java 11) but you're trying to execute with an old java...
### Verify * if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue * the version of java ``` openjdk 11.0.11 2021-04-20 OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.18.04) OpenJDK...
### Illegal Capacity: -4 I am trying to run wgscoverageplotter for 1956 contigs. I get the following error: `[INFO][WGSCoveragePlotter]Count: 1,927 Elapsed: 19 minutes(98.61%) Remains: 16 seconds(1.39%) Last: tig00109025:1 [INFO][WGSCoveragePlotter]. Completed....
